Variant report

Variant	rs6533344
Chromosome Location	chr4:78852682-78852683
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 62 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:51)

rs_ID	r²[population]
rs10033527	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10033613	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs1021824	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1021826	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11097938	0.91[CHB][hapmap];1.00[JPT][hapmap];0.88[MKK][hapmap]
rs11729215	0.95[CHB][hapmap];0.83[CHD][hapmap];1.00[JPT][hapmap];0.80[MEX][hapmap];0.80[MKK][hapmap]
rs12641050	0.81[ASN][1000 genomes]
rs12645742	0.91[CHB][hapmap];1.00[JPT][hapmap]
rs13101418	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];0.97[GIH][hapmap];0.94[JPT][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs13101987	0.91[CHB][hapmap];1.00[JPT][hapmap];0.80[MEX][hapmap]
rs13103035	0.91[CHB][hapmap];1.00[JPT][hapmap]
rs13103523	0.87[CHB][hapmap];1.00[JPT][hapmap]
rs13106067	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs13114091	0.81[ASN][1000 genomes]
rs13120272	0.87[CHB][hapmap];1.00[JPT][hapmap];0.88[MKK][hapmap]
rs16996915	0.95[CHB][hapmap];0.83[CHD][hapmap];1.00[JPT][hapmap];0.84[MKK][hapmap]
rs17002849	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2088992	0.83[CEU][hapmap];0.81[CHB][hapmap];0.89[JPT][hapmap]
rs28404443	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs34459497	0.82[EUR][1000 genomes]
rs34751953	0.85[AMR][1000 genomes];0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs34850103	0.81[ASN][1000 genomes]
rs35648590	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs35979107	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4453957	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs4571357	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4577601	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.82[MKK][hapmap];1.00[TSI][hapmap];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4859509	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4859511	0.95[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4859877	0.95[CHB][hapmap];1.00[JPT][hapmap]
rs4859879	0.91[CHB][hapmap];1.00[JPT][hapmap];0.84[MKK][hapmap]
rs4859888	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4859889	0.82[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.84[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.81[MKK][hapmap];0.97[TSI][hapmap];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs62302728	0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs62302732	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6533282	0.94[CEU][hapmap];0.95[CHB][hapmap];0.93[JPT][hapmap];0.87[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs6533291	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs6533345	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs66825464	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6811736	0.86[CEU][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6814912	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap];0.92[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6845998	0.81[ASN][1000 genomes]
rs6848029	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6854895	1.00[CEU][hapmap];0.91[CHB][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7670157	0.90[CHB][hapmap];0.84[CHD][hapmap];0.89[JPT][hapmap];0.90[TSI][hapmap];0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7675009	0.81[CEU][hapmap];0.95[CHB][hapmap];0.83[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.92[TSI][hapmap]
rs7676660	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7695874	0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7698627	0.95[CEU][hapmap];0.95[CHB][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.80[MEX][hapmap];0.92[TSI][hapmap];0.87[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs7698629	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs905376	0.95[CEU][hapmap];0.92[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:11 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv879501	chr4:78647634-78866007	Active TSS Flanking Active TSS Strong transcription Weak transcription Enhancers ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
2	esv2752050	chr4:78693311-78975321	Enhancers Weak transcription Flanking Active TSS Bivalent/Poised TSS Strong transcription Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
3	nsv1010714	chr4:78742505-78991030	Weak transcription Genic enhancers Bivalent/Poised TSS Enhancers Strong transcription Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
4	nsv516836	chr4:78748977-78981919	Strong transcription Flanking Active TSS Weak transcription Active TSS Enhancers Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
5	nsv594704	chr4:78748977-78981919	Strong transcription Enhancers Weak transcription Bivalent/Poised TSS Genic enhancers Active TSS Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
6	nsv461562	chr4:78757015-78981919	Enhancers Weak transcription Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Flanking Active TSS Active TSS Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
7	nsv461563	chr4:78757015-78981919	Strong transcription Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Enhancers Weak transcription Active TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
8	nsv594705	chr4:78757015-78981919	Enhancers Genic enhancers Strong transcription Weak transcription Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
9	nsv1008217	chr4:78777531-78957311	Strong transcription Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
10	nsv537145	chr4:78777531-78957311	Active TSS Enhancers Strong transcription Weak transcription Genic enhancers ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
11	nsv534024	chr4:78785189-79437403	ZNF genes & repeats Flanking Active TSS Enhancers Active TSS Weak transcription Strong transcription Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs6533344	MRPL1	cis	multi-tissue	Pritchard
rs6533344	C4orf26	cis	parietal	SCAN
rs6533344	MRPL1	cis	lymphoblastoid	seeQTL
rs6533344	MRPL1	cis	cerebellum	SCAN
rs6533344	FRAS1	cis	parietal	SCAN

Chromatin state (count:103 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:78784800-78859800	Weak transcription	Esophagus	oesophagus
2	chr4:78785000-78874400	Weak transcription	Right Ventricle	heart
3	chr4:78802400-78858400	Weak transcription	Aorta	Aorta
4	chr4:78806000-78881000	Weak transcription	Brain Hippocampus Middle	brain
5	chr4:78806600-78875600	Weak transcription	Colonic Mucosa	Colon
6	chr4:78809600-78865400	Weak transcription	HUES6 Cell Line	embryonic stem cell
7	chr4:78809600-78881200	Weak transcription	Rectal Smooth Muscle	rectum
8	chr4:78814600-78874400	Weak transcription	Pancreas	Pancrea
9	chr4:78816400-78866400	Weak transcription	Fetal Thymus	thymus
10	chr4:78816400-78876000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
11	chr4:78816600-78875800	Weak transcription	Rectal Mucosa Donor 31	rectum
12	chr4:78818800-78872800	Weak transcription	Sigmoid Colon	Sigmoid Colon
13	chr4:78821000-78866000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
14	chr4:78821400-78873200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
15	chr4:78830000-78866600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
16	chr4:78830400-78877000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
17	chr4:78831800-78865800	Weak transcription	Duodenum Mucosa	Duodenum
18	chr4:78832000-78858000	Weak transcription	Fetal Stomach	stomach
19	chr4:78833600-78865400	Weak transcription	Fetal Kidney	kidney
20	chr4:78834000-78852800	Weak transcription	HUES64 Cell Line	embryonic stem cell
21	chr4:78842200-78865600	Weak transcription	H1 Cell Line	embryonic stem cell
22	chr4:78842400-78865400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
23	chr4:78843800-78852800	Weak transcription	Placenta	Placenta
24	chr4:78843800-78854200	Weak transcription	Gastric	stomach
25	chr4:78843800-78858000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
26	chr4:78843800-78858000	Weak transcription	Left Ventricle	heart
27	chr4:78843800-78865200	Weak transcription	Psoas Muscle	Psoas
28	chr4:78844200-78871400	Weak transcription	NHDF-Ad	bronchial
29	chr4:78845200-78856000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
30	chr4:78847400-78853000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
31	chr4:78847400-78860200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
32	chr4:78847600-78852800	Weak transcription	K562	blood
33	chr4:78847600-78865200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
34	chr4:78848000-78856400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
35	chr4:78848800-78869000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
36	chr4:78849400-78853400	Enhancers	HUVEC	blood vessel
37	chr4:78849400-78876600	Weak transcription	Colon Smooth Muscle	Colon
38	chr4:78849600-78871400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
39	chr4:78849600-78881000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
40	chr4:78849800-78852800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
41	chr4:78849800-78858800	Weak transcription	Duodenum Smooth Muscle	Duodenum
42	chr4:78850200-78881000	Weak transcription	A549	lung
43	chr4:78851000-78853000	Strong transcription	GM12878-XiMat	blood
44	chr4:78851000-78854200	Strong transcription	Primary T cells fromperipheralblood	blood
45	chr4:78851000-78857200	Weak transcription	Brain Angular Gyrus	brain
46	chr4:78851200-78853000	Strong transcription	Spleen	Spleen
47	chr4:78851200-78853200	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
48	chr4:78851200-78853200	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
49	chr4:78851200-78853600	Strong transcription	Primary T helper cells PMA-I stimulated	--
50	chr4:78851200-78853800	Strong transcription	Primary T helper naive cells fromperipheralblood	blood

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